March 19, 2013

High-quality Neandertal genome online

The Max Planck institute has posted their high-coverage Neandertal genome on their site. The data can be downloaded from here. They had done the same with the high-quality Denisova genome, and it's great that they're making data available ahead of the official scientific publication, as this allows others to start using it much earlier.

From their site:

The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010. The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.

It then appears that Neandertals occupied the same cave as the elusive Denisovans. When? I guess we'll have to wait to find out, but the preliminary genetic analysis shown on the figure (top-left) makes it clear that the "Altai" specimen marked in red which is the source of the high-coverage Neandertal genome does indeed group with other Neandertals, while Denisova is more related to Neandertals than to modern humans.

I've highlighted this before, but it bears repeating: divergence between Neandertals and Denisovans --who were in the same place (Denisova cave), perhaps some thousands of years apart-- seems to exceed that found between any two modern human groups which span the entire Earth.

6 comments:

"divergence between Neandertals and Denisovans --who were in the same place (Denisova cave), perhaps some thousands of years apart"

Not too many 'thousands of years apart' though. Aren't the remains of the two species at Altai dated to within 4-5000 years of each other? I find no problem with the species sharing the geographic range, or even living together. And 'modern' humans may have been part of the mix there too.

I am really interested in the y-DNA and its relationship to the human root and Chimpanzees (as an outgroup)!

This probably was roughly the time when Neanderthals were just reaching their eastern boundary - but I am convinced long before them, heidelbergensis made it all the way to East Asia. At any rate, it appears that Neanderthals did not have any significant advantage over other humans during that time. So, unlike the dominance of (relatively late) modern humans, it appears there was pretty much a stalemate between different groups, with occasional small amounts of gene flow.

As to the similarity of all Neanderthals (and their late branching), one also has to consider the preservation bias: most samples for a while will be from about the last time slice of when Neanderthals lived.

"The more surprising point, in my mind, is that Denisova shares a clade with Neanderthals that modern humans do not".

Why do you find that 'surprising'. Surely both are 'northern' species while H. sapiens is 'African'. Either the common ancestor of Denisovans and Neanderthals moved out of Africa some time before H. sapiens did, or the ancestor of H. sapiens moved into Africa from Eurasia before some of them moved back out.

The more surprising point, in my mind, is that Denisova shares a clade with Neanderthals that modern humans do not.

Andrew -

No, this has not changed from the previous, rougher Neanderthal DNA sequence.

That's also why not just I but also the original authors mentioned heidelbergensis as a possibility for Denisovans. If contact between Africans and Europeans/ Levantines became sparse after ~800,000 years ago, and seized to exist after ~400,000 - 350,000 ya due to climate, then heidelbergensis begat very early Neanderthals just shortly after contact to African humans became unimportant (until ~130,000 ya).

"That's also why not just I but also the original authors mentioned heidelbergensis as a possibility for Denisovans".

I'm inclined to that belief too. But I've just realised why Andrew is so surprised by the Neanderthal/Denisova close connection. It doesn't fit the idea that Melanesians picked up their Denisova element in Southeast Asia. I have long been suspicious of any ancient Denisova presence in SE Asia as to me it seems unlikely the SE Asian H. erectus would be genetically the same as Altai H. erectus. Under the heidelbergensis view that differentiation becomes even more likely. Heidelbergensis didn't make it to SE Asia at all, or at least only at a very minor level.

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